"The (Roman Catholic) Church is profoundly and irrevocably committed to reject all anti-Semitism and to continue to build good and lasting relations between our two communities."
Benedict sparked anger last month when he lifted excommunications on Richard Williamson, an ultra-traditionalist bishop, who denies gas chambers were used in the Holocaust, and three other bishops.
Benedict has said he was not aware of Williamson's denial of the Holocaust when he lifted the excommunication orders.
The Vatican has since ordered Williamson, a member of the Society of St Pius X, to publicly recant his views.
Thursday's conference was Benedict's first meeting with Jews since the row began in January.
He recalled his own visit to the death camp at Auschwitz in 2006, saying: "It is my fervent prayer that the memory of this appalling crime will strengthen our determination to heal the wounds that for too long have sullied relations between Christians and Jews."
Rabbi Arther Schneier, in an address to Benedict at the conference, thanked him for understanding their pain.
"As a Holocaust survivor, these have been painful and difficult days, when confronted with Holocaust denial by no less than a bishop of the Society of St Pius X," he said.
'Pain and anguish'
Schneier said victims of the Holocaust "have not given us the right to forgive the perpetrators nor the Holocaust deniers. Thank you for understanding our pain and anguish ...".
He and Benedict both said they hoped dialogue between the two faiths could become stronger.
Benedict also announced he was preparing to visit Israel, which would be the first papal visit since John Paul visited in 2000.
The Vatican said the trip is expected for May.